After studying medicine at the University of Berlin, Schwann began his
most important work, the microscopic study of animal tissue, which led
to his idea that all living things are made up of cells and that each
cell contains essential components such as a nucleus. He published
this idea in Microscopic Researches into Accordance in the Structure and
Growth of Animals and Plants (1839).

After an education in law, Schleiden concentrated on botanical
studies. In 1838, one year before Schwann, he developed the idea that
the cell was the basic unit of plants and that growth consisted of
production and development of new cells. Schleiden's two-volume text
Principles of Scientific Botany (1842-43) was long a model
for modern botanical works. The cell theory was extended by others
and drew the attention of biologists to the study of cell contents.

The Cell Theory-Proposed by Schleiden & Schwann in 1839, stated
All organisms are composed of one or more cells.
and The cell is the basic organizational unit of life.

Later, in 1859, Virchow proposed that all living cells arise from
pre-existing cells (except the very first cell!)

In 1862, Louis Pasteur proved Virchow's proposal by the long neck
Flask experiment.

Today scientists know that living things are made up of cells that
are made by chemical compounds, and yet they are able to proliferate
and make new cells. There are, however, two classes of cells-
The eucaryotes and procaryotes- the main difference being that
procaryotes have no membrane bound organelles.

PROCARYOTES- Belong to the kingdom Monera with two series of
Archaeobacteria and Eubacteria. These cells lack nuclear membrane,
mitochondria, endoplasmic reticulum, golgi body and lysosomes.
They replicate by binary fission. Procaryotes do not have centrosome.
Procaryotes/bacteria, however, like eukaryotes, contain both DNA and RNA,
ribosomes, digestive enzymes, and are able to generate ATP. The
characteristics of bacteria are as follows:

2. Cell Wall- Bacteria cell wall consists of Muriens, a polymer of
polysaccharides, and the amino acid Muramic acid. The cell wall of
the bacteria is the site where antibiotics work by promoting disassembly
of the bacterial cell wall. Another characteristic of the cell wall
is its chemical reactivity to various stains, which helps their classification
and recognition.

Capsule- A mucoid polysaccharide that is secreted by some bacterial
cells. It helps to protect the cell from the host's immune system in cases
of infections.

Endospores- This is a form that a bacteria may take to protect itself from
physical harm. The endospore contains both DNA and any other vital agents
required for normal living. These endospores can tolerate extreme heat
and dryness for long period of time.

3. Reproduction- Even though bacteria do not contain a nucleus, they
have a nuclear regions or Nucleoid. Nucleoid is a site where the single
strand of circular DNA-isolated chromosomes-is located. Bacteria reproduce
at a very high rate (as low as once every 20 minutes) through binary
fission. Reproduction is not by mitosis like in eucaryotic cells. The two
new daughter cells have the same genetic information as the parental cell
except that the daughter cells now have half of the original amount
of cytoplasm and surface area.

4. Motility- Bacteria contain flagella for locomotion. This flagella
has a rotatory motion as a result of the movement of H+ ions down
their electrochemical gradient through specific channels at the
base of the flagella. Bacterial flagella have no structural similarity to
the eukaryotic flagella. Bacterial flagella arise from basal granules.

5. Pilli-Serves as an appendage on the surface of either motile or
non-motile cells. Pilli function as either a grasping agents for the
bacteria to the host cell or medium, or may function as conjugating
tubes for transfer of DNA between two bacteria within the same
species. Pilli also function in absorbing nutrition for the bacteria
from the environment or the host cell. ...

6. Photosynthesis- Chemosynthetic bacteria acquire their energy through
oxidizing inorganiccompounds-like sulfur, nitrite, and ferrous ion.
The nitrifying bacteria belong to this group and it has an important
function in the nitrogen cycle. However, some of the bacteria
are autotrophic-namely they acquire energy via photosynthesis. These are:

A. Green And Purple Bacteria- Anaerobic bacteria that have light
trapping compounds in their Chromatophores. This chromatophore provides
energy for the bacteria via Photosystem I. Green and Purple bacteria
carry their "Dark" reaction photosynthesis in the cytoplasm.

B. Halophillic Archeo Bacteria-These are bacteria that live in the
salt lakes and brines. They use Rhodopsin-like pigments instead of
chlorophyll in their plasma membrane. In an anaerobic condition these
pigmented molecules in the presence of light release the internal
H+, hence creating a H+ gradient that will produce ATP. This ATP is
then used for bacterial energy.

C. Cyanobacters- These are photosynthetic bacteria with their chlorophyll
A within the Thylakoid membranes. Oxygen is the end product of their
photosynthesis. Cyanobacters are thought to be the father of eucaryotic
chloroplasts.

Note:The characteristic color of Blue-Green bacteria is due to the
presence of Phycoerythin (red) and phycocyanin (blue).

D. Nutrition- Bacteria are mostly heterotrophs, namely they are either
parasitic or saprophytic. A majority of bacteria are Aerobic, namely
they require O2 for their final electron acceptor in their electron
transport system. Note: The Electron Transport System (ETS) of bacteria
are held on the inside plasma membrane or on its invagination. ...

Cell Metabolism

A. Metabolism- It is the total energy that is released
and consumed by a cell. Metabolism is the sum of the total energy
of catabolism and anabolism.

1. Catabolism- The energy releasing process in which a chemical
(food) is broken down, via decomposition or degradation, into its
smaller constituents. An example is the breakdown of glucose into
CO2 and water and 38 molecules of ATP.

2. Anabolism- Anabolism is the opposite of catabolism. In this
class of metabolism, the cell consumes energy to produce larger
molecules via smaller ones. An example is the synthesis of
glycogen from glucose and ATP.

Note: The produced energy in catabolism may be used to provide heat
energy for other cellular catabolism or anabolism. Yet, some of the
energy that is used by anabolism may be used later for catabolism.
Example. glycogen is an storage site for both glucose and ATP since,
when glucose is released from glycogen, the sugar molecule can be
used by the cell to produce 38 ATP via catabolism.

ENERGY RICH MOLECULES- In a cellular respiration there are three
kinds of energy rich molecules. These are ATP, NADH2 and FADH2.
However, for NADH2 and FADH2 molecules to be useful by the cell
they are both converted, via other mechanisms, into ATP.

1. Adenosine Triphosphate-This is the most common energy carrier
molecule in respiration. It is used in cellular respiration,
metabolism, catabolism, neuron action potentials and muscle contractions
as examples. Its structure is :

The ATPase is consumed and can be broken down into ADP and AMP
via hydrolysis;

Phosphorylation of adenosine monophosphate is a process whereby
the low energy AMP formed creates a higher energy bond ADP and ATP.

2. Flavin Adenine Dinucleotide (FAD)-Another molecule that is used by
cellular respiration to carry energy from one place to another.
FAD is used in the Kreb's Cycle.

Every molecule of FADH2 has the energy equivalent of 2 molecules of ATP.

3. Nicotinamide Adenine Dinucleotide (NADH)-After ATP, NADH is the
second most commonly used energy carrier.

Every molecule of NADH2 has enough energy to promote 3 molecules of ATP.

I. Glycolysis- Or anaerobic respiration, is the process that occurs in
either the absence or presence of oxygen molecules in the cytoplasm of
a cell. The process starts when a glucose molecule is phosphorylated
and is broken down into two 3 carbon molecules of pyruvic acid. In
this process 2 molecules of ATP start the hydrolysis and via subsequent
steps 2 molecules of ATP and 2 molecules of NADH2 are produced, resulting
in total production of 2 ATP molecules to be used by the cells energy.
Note: The energy stored in NADH2 (equivalent to 6 ATP molecules) is
used again by the Kreb's cycle itself. Thus this energy is not counted
toward glycolysis energy release. Glycolysis is as follows:

II. Fermentation- This step occurs in eucaryotes only when there is a
shortage of oxygen. It occurs in anaerobic and facultative aerobic bacteria,
for instance.

1. In Muscle Cells- During extraneous activities, the oxygen in the
muscle tissue is decreased to an extent that aerobic respiration does
not occur at a sufficient rate. Hence;

2. In Yeast- The fermentation end product is ethyl alcohol;

Note: In fermentation, pyruvic acid is the final electron acceptor. Also,
when oxygen is present in the lactic acid accumulated muscle cells, then,
via the enzyme lactate dehydriogenase the lactic acid is converted back
into pyruvic acid to be used again in oxidation respiration.

III. Aerobic Metabolism- Or aerobic respiration, is the process that
occurs only in the mitochondria. This is the most energy yielding chemical
reaction within the cell. Namely 36 of 38 ATP are produced in the
mitochondria, hence its nick name " The cell's Powerhouse". There are
three stages where oxidation respiration occurs. 1. Production of Acetyl-COA
from pyruvic acid. 2. Tricarboxylic acid cycle. 3. Electron Transport system

1. Acetyl-Coa Pathway- This is a cycle where a single molecule of pyruvic
acid is bonded to a molecule of coenzyme-A, and the released energy forms
a molecule of NADH2+. Yet, the pyruvic acid in the process has lost its
carboxylic acid end in the form of CO2 gas. The end product is called
Acetyl-COA.

Note: The prefix 2 is written because a 6 carbon sugar molecule yields
2 molecules of pyruvic acid. Thus, from here on the prefix 2 represents
the total molecules in each step produced from theoriginal single molecule
of glucose.

2. Tricarboxylic Acid Cycle (Tca)- Or the Kreb's or Citric Acid Cycle.
This is the cycle where Acetyl-COA binds to an Oxaloacetic acid (from
the cycle) to form a citric acid, the initiating molecule of the TCA cycle.
The TCA cycle produces 24 ATP molecules. The cycle is as follows:

SUMMARY: The three stages of energy liberating pathway of glucose metabolism
can be written in the form: ...

IV. Electron Transport System (ETS)- This is a system that is the most
complicated of all, whereby the energy stored in the NADPH2+ and
FADH2+ molecule is released via different steps so that molecules of ADP
and Pi are combined to form ATP molecules. All of the processes in this
system occur within the inner mitochondrial membrane, via various enzymes
and protein changes. It should be noted that the whole process is to use
the energy stored in either NADH2+ and FADH2+ and consume it to create a
concentration gradient of H+ between the outer mitochondrial membrane
compartment (higher H+ concentration) and inner mitochondrial membrane
compartment. The process is as follows:

1. When NADH2+ binds to the flavoprotein (FP) it reduces an e- and a H+. Two H+
are released into the outer mitochondrial matrix, while the electron moves along
the proteins of the inner mitochondrial membrane.

2. Two electrons are bounded to the flavoprotein then these two electrons move
from FP to the protein containing iron and sulfur (FeS + FeSB), then to the
cytochrome b. Cytochrome b gives the e- to the coenzyme Q (Q).

3. Coenzyme Q is an enzyme that moves across the inner matrix membrane
when it carries an e- within . This movement also transports 2H+ to the
outer matrix membrane.
Again e- moves from Q to cytochrome b2----> Cyt e-------> Cyt a and Cyt a3.

With the exception that 2H+ molecules are imported into the outer membrane
matrix from inner membrane matrix. B. The electron when it reaches Cyt a3 is
absorbed by highly electronegative oxygen and 2 H+ to form a water molecule.

4. Due to the consumption of energy by ETS the e- has the highest energy when
it is at FP, and it loses energy as it goes down the ETS until it reaches
the Cyt a3.

5. ATP permease- This is a pump that is used by the inner matrix membrane to
bring H+ and ADP+ Pi into the inner matrix from outer matrix, and yet the ATP
permease functions in exporting the newly synthesized ATP + OH- from the
inner matrix to the outer matrix.

6. The last but the most important enzyme on the pathway is the F complex
or the ATP permease. This enzyme uses the electrochemical gradient between
the outer membrane matrix and inner membrane matrix to synthesize ATP from
ADP + Pi. For every inflow of a pair of H+ there will be a new ATP synthesized.

7. If you add the highlighted number of H+ in the paragraphs 1 and 3 you
will see that a single molecule of NADH2+ initiates the release of 6H+ from
the inner membrane matrix to the outer membrane matrix. Thus when 3 pairs of
H+ are imported back from the outer membrane matrix there will be 3 ATP
molecule synthesized.

8. In the case of FADH2, the lower energy FADH2 molecule will bind the
electron transport system at coenzyme Q. This results in the export of
2 pairs of H+ from the inner matrix to the outer matrix (4H+ in paragraph
3 only). As a result there will be only 2 ATP produced.
Note: The inner matrix membrane without its ATP permease and ATP synthase
is not permeable to the passage of H+. Thus the outer membrane matrix is
positively charged with an electrochemical gradient and osmotic pressure
with respect to the negatively charged inner matrix....

Respiration LinksRespiration - The Basic Reaction

O2 +

Carbohydrate & OtherOrganic Compounds*

+ ---

Living Cells

---

ATP& Heat*

+ CO2 + Water

Overview of Respiration (See Lewis fig. 7.5)

Organic Compounds*From Food

---

Glycolysis(EnzymeReactionsin Cytoplasm)

---

PyruvicAcid*some ATP*

---------

Krebs Cycle(Enzyme Reactionsin Mitochondria)

---

NADH*& CO2

---

ProtonGradient*

---

LotsofATP*

Glucose* Activation (use of ATP*)

Enzyme Reactions

Energy Extraction (Production of ATP* & NADH*)

Production of Pyruvic Acid*

Mitochondrion Structure
(see Lewis, figures 7.7 & 7.14)

Outer membrane

Inner membrane systems

Cristae

Electron Carriers of repiratory chain

ATP Synthase

Matrix (liquid area within the inner membrane)

Enzymes of Krebs Cycle)

DNA

Ribosomes

Intermembrane space (liquid area between the inner and outer membranes)

pro = before, karyon = a little nut (what nuclei looked like to those who
first saw them through a microscope)

cells without organized nuclei bounded by a nuclear membrane

cell wall

no membrane bound organelles

nucleoid

Eukaryotic Cells

eu = true, karyon = a little nut (nucleus)

cells with organized nuclei bounded by a nuclear membrane

cell wall in some

plasma membrane in all

membrane bound nucleus

membrane bound organelles

endoplasmic reticulum (ER)

ribosomes

golgi bodies

mitochondria

chloroplasts

Cell Organelles

Nucleus
This is where the DNA is kept and RNA is transcribed. RNA is
transported out of the nucleus through the nuclear pores. Proteins
needed inside the nucleus are transported in through the nuclear
pores. The nucleolus is usually visible as a dark spot in the nucleus
(note the dark nucleolus in this electron microscope photo of a nucleus),
and is the site of ribosome formation.

Ribosomes
Ribosomes are the sites of protein synthesis, where RNA is
translated into protein. Protein synthesis is extremely important to
cells, and so large numbers of ribosomes are found throughout cells
(often numbering in the hundreds or thousands). Ribosomes exist
floating freely in the cytoplasm, and also bound to the endoplasmic
reticulum (ER). ER bound to ribosomes is called rough ER because the
ribosomes appear as black dots on the ER in electron microscope photos,
giving the ER a rough texture. These organelles are quite small,
made up of 50 proteins and several long RNAs intricately bound together.
Ribosomes have no membrane. Ribosomes disassemble into two subunits
when not actively synthesizing protein..

Mitochondria
Mitochondria (singular: mitochondrion) are the sites of aerobic
respiration, and generally are the major energy production center
in eukaryotes. Mitochondria have two membranes, an inner and an outer,
clearly visible in this electron microscope photo of a mitochondrion.
Note the reticulations, or many infoldings, of the inner membrane,
This serves to increase the surface area of membrane on which membrane-
bound reactions can take place. The existence of this double membrane
has led many biologists to theorize that mitochondria are the descendants
of some bacteria that was endocytosed by a larger cell billions of years
ago, but not digested. This fascinating theory of symbiosis, which might
lend an explanation to the development of eukaryotic cells, has
additional supporting evidence. Mitochondria have their own DNA and
their own ribosomes; and those ribosomes are more similar to bacterial
ribosomes than to eukaryotic ribosomes..

Chloroplasts
These organelles are the site of photosynthesis in plants and other
photosynthesizing organisms. They also have a double membrane. There
is a more complete description of the chloroplast here, in the
chapter on photosynthesis..

Endoplasmic Reticulum (ER)
The ER is the transport network for molecules targeted for certain
modifications and specific final destinations, as opposed to molecules
that are destined to float freely in the cytoplasm. There are two
types of ER, rough and smooth. Rough ER has ribosomes attached to it,
and smooth ER does not.

Golgi apparatus
This organelle modifies molecules and packages them into small membrane
bound sacs called vesicles. These sacs can be targetted at various
locations in the cell and even to its exterior.

Lysosome
This organelle digests waste materials and food within the cell,
breaking down molecules into their base components with strong digestive
enzymes. Here we can see an advantage of the compartmentalization of
the eukaryotic cell: the cell could not support such destructive enzymes
if they were not contained in a membrane-bound lysosome.